public IEnumerable <SkylineDocumentProto.Types.LinkedIon> GetLinkedIonProtos()
{
foreach (var child in Children)
{
var proto = new SkylineDocumentProto.Types.LinkedIon()
{
ModificationIndex = child.Item1.IndexAa,
ModificationName = child.Item1.ModName
};
if (child.Item2.IsOrphan)
{
proto.Orphan = true;
}
else
{
proto.IonType = DataValues.ToIonType(child.Item2.IonType);
proto.Ordinal = child.Item2.Ordinal;
}
proto.Children.AddRange(child.Item2.GetLinkedIonProtos());
yield return(proto);
}
}
public SkylineDocumentProto.Types.Transition ToTransitionProto(SrmSettings settings)
{
var transitionProto = new SkylineDocumentProto.Types.Transition
{
FragmentType = DataValues.ToIonType(Transition.IonType),
NotQuantitative = !ExplicitQuantitative
};
if (Transition.IsCustom() && !Transition.IsPrecursor())
{
SetCustomIonFragmentInfo(transitionProto);
}
transitionProto.DecoyMassShift = DataValues.ToOptional(Transition.DecoyMassShift);
transitionProto.MassIndex = Transition.MassIndex;
if (HasDistInfo)
{
transitionProto.IsotopeDistRank = DataValues.ToOptional(IsotopeDistInfo.Rank);
transitionProto.IsotopeDistProportion = DataValues.ToOptional(IsotopeDistInfo.Proportion);
}
if (!Transition.IsPrecursor())
{
if (!Transition.IsCustom())
{
transitionProto.FragmentOrdinal = Transition.Ordinal;
transitionProto.CalcNeutralMass = GetMoleculePersistentNeutralMass();
}
transitionProto.Charge = Transition.Charge;
if (!Transition.Adduct.IsProteomic)
{
transitionProto.Adduct = DataValues.ToOptional(Transition.Adduct.AsFormulaOrSignedInt());
}
if (!Transition.IsCustom())
{
transitionProto.CleavageAa = Transition.AA;
transitionProto.LostMass = LostMass;
}
}
if (Annotations != null)
{
transitionProto.Annotations = Annotations.ToProtoAnnotations();
}
transitionProto.ProductMz = Mz;
if (Losses != null)
{
foreach (var loss in Losses.Losses)
{
var neutralLoss = new SkylineDocumentProto.Types.TransitionLoss();
if (loss.PrecursorMod == null)
{
neutralLoss.Formula = loss.Loss.Formula;
neutralLoss.MonoisotopicMass = loss.Loss.MonoisotopicMass;
neutralLoss.AverageMass = loss.Loss.AverageMass;
neutralLoss.LossInclusion = DataValues.ToLossInclusion(loss.Loss.Inclusion);
neutralLoss.Charge = loss.Loss.Charge;
}
else
{
neutralLoss.ModificationName = loss.PrecursorMod.Name;
neutralLoss.LossIndex = loss.LossIndex;
}
transitionProto.Losses.Add(neutralLoss);
}
}
if (HasLibInfo)
{
transitionProto.LibInfo = new SkylineDocumentProto.Types.TransitionLibInfo
{
Intensity = LibInfo.Intensity,
Rank = LibInfo.Rank
};
}
if (Results != null)
{
transitionProto.Results = new SkylineDocumentProto.Types.TransitionResults();
transitionProto.Results.Peaks.AddRange(GetTransitionPeakProtos(settings.MeasuredResults));
}
if (!Equals(ExplicitValues, ExplicitTransitionValues.EMPTY))
{
transitionProto.ExplicitCollisionEnergy = DataValues.ToOptional(ExplicitValues.CollisionEnergy);
transitionProto.ExplicitConeVoltage = DataValues.ToOptional(ExplicitValues.ConeVoltage);
transitionProto.ExplicitDeclusteringPotential = DataValues.ToOptional(ExplicitValues.DeclusteringPotential);
transitionProto.ExplicitIonMobilityHighEnergyOffset = DataValues.ToOptional(ExplicitValues.IonMobilityHighEnergyOffset);
transitionProto.ExplicitSLens = DataValues.ToOptional(ExplicitValues.SLens);
}
return(transitionProto);
}